K-Means notes

K-means is currently trying to identify 4 clusters using 3 dimensions (CCR7, CD45R4, and CD28)
The input to k-means is currently the union of Helper and Cytotoxic T cells
- For current results below, only OpenCyto was used to determine input for kmeans clustering (i.e did not start with Helper/Cyto T defined by manual .wsps)

Control gating “consistency”

OC controls were filtered for likely failures (lose ~%10 of the samples with this filter)

Control summary for results

CONTROL	N_FCS
A	35
B	14
C	32
D	28
E	31
F	19
G	21
H	26

	KEYFCS	SAMPLE	POPULATION	COUNT	PARENT_COUNT	OPTIMAL_K	DFK_ALL	NUM_POPS_ASSIGNED	TOTAL_COUNTS	QC	PANEL	MACHINE	LAB_ID	formatName	DATE	DATE_MONTH	DATE_WEEK	formatExp	EXPERIMENTER	SANITIZE_NAME	MANUAL_ANNOTATION	PARENT_FREQ	PARENT_PERCENT	KEY	CTL	Study.ID	variable	value
61	2016-05-17_PANEL 1_DHS_panel one_Ctl-D_016.fcs_CYTO_central memory	2016-05-17_PANEL 1_DHS_panel one_Ctl-D_016.fcs	CYTO_central memory	14145	77632	3	1,0.832408640742792,0.738543623520837,0.93952748979841,1.03783470428523,0.963218817742073	4	592897	FALSE	panel1	LSR	NA	2016-05-17_PANEL 1_DHS_panel one_Ctl-D_016.fcs	2016-05-17	2016-05-01	2016-05-16	2016-05-17_PANEL 1_DHS_panel one_Ctl-D_016.fcs	DHS	2016-05-17_PANEL_1_DHS_panel_one_Ctl-D_016.fcs	FALSE	0.1822058	18.22058	NA_CYTO_central memory	D	2016-05-17_PANEL 1_DHS_panel one_Ctl-D_016.fcs	CYTO_central memory	3679
136	2016-05-25_PANEL 1_ZF_panel one_Ctl-D_011.fcs_CYTO_central memory	2016-05-25_PANEL 1_ZF_panel one_Ctl-D_011.fcs	CYTO_central memory	10249	61254	3	1,0.892101597249016,0.654241194410193,0.954480334434967,1.00710806266813,0.992861258109737	4	486931	FALSE	panel1	LSR	NA	2016-05-25_PANEL 1_ZF_panel one_Ctl-D_011.fcs	2016-05-25	2016-05-01	2016-05-23	2016-05-25_PANEL 1_ZF_panel one_Ctl-D_011.fcs	ZF	2016-05-25_PANEL_1_ZF_panel_one_Ctl-D_011.fcs	FALSE	0.1673197	16.73197	NA_CYTO_central memory	D	2016-05-25_PANEL 1_ZF_panel one_Ctl-D_011.fcs	CYTO_central memory	1754
211	2016-06-06_PANEL 1_DHS_Group two_Ctl-D_033.fcs_CYTO_central memory	2016-06-06_PANEL 1_DHS_Group two_Ctl-D_033.fcs	CYTO_central memory	15047	71831	3	1,0.935366407885674,0.695950006331655,0.959086114450938,1.0199350965884,1.00919291748581	4	672423	FALSE	panel1	LSR	NA	2016-06-06_PANEL 1_DHS_Group two_Ctl-D_033.fcs	2016-06-06	2016-06-01	2016-06-06	2016-06-06_PANEL 1_DHS_Group two_Ctl-D_033.fcs	DHS	2016-06-06_PANEL_1_DHS_Group_two_Ctl-D_033.fcs	FALSE	0.2094778	20.94778	NA_CYTO_central memory	D	2016-06-06_PANEL 1_DHS_Group two_Ctl-D_033.fcs	CYTO_central memory	1258
436	2016-07-18_PANEL 1_DHS_Group two_Ctl-D_033.fcs_CYTO_central memory	2016-07-18_PANEL 1_DHS_Group two_Ctl-D_033.fcs	CYTO_central memory	9335	49458	3	1,0.853732498839986,0.745609378709498,0.957623877881171,1.03205307917842,1.02001671277786	4	432309	FALSE	panel1	LSR	NA	2016-07-18_PANEL 1_DHS_Group two_Ctl-D_033.fcs	2016-07-18	2016-07-01	2016-07-18	2016-07-18_PANEL 1_DHS_Group two_Ctl-D_033.fcs	DHS	2016-07-18_PANEL_1_DHS_Group_two_Ctl-D_033.fcs	FALSE	0.1887460	18.87460	NA_CYTO_central memory	D	2016-07-18_PANEL 1_DHS_Group two_Ctl-D_033.fcs	CYTO_central memory	3377

Correlations to manual 1st 1k